Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins
annotate macros.xml @ 22:9d93c8fbe0a6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
author | iuc |
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date | Thu, 05 Dec 2024 18:29:04 +0000 |
parents | f72063d9426b |
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a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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1 <macros> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> |
22
9d93c8fbe0a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
iuc
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3 <token name="@TOOL_VERSION@">3.7.6</token> |
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f72063d9426b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03
iuc
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4 <token name="@VERSION_SUFFIX@">1</token> |
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11fa44ee0603
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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5 <token name="@PROFILE@">23.0</token> |
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8926550196ce
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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6 <token name="@USE_RANGE@"> |
8926550196ce
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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7 #if $use_range.select_use_range == "yes_use_range": |
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9e357a8b2ec3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3e5c2f8ce3e540b0474746a33ee20b4a374dd38c"
iuc
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8 --range $use_range.range_min:$use_range.range_max |
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8926550196ce
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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9 #end if |
8926550196ce
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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10 </token> |
8926550196ce
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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11 |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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12 <xml name="requirements"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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13 <requirements> |
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03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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14 <requirement type="package" version="@TOOL_VERSION@">hicexplorer</requirement> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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15 <yield /> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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16 </requirements> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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17 <version_command>@BINARY@ --version</version_command> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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18 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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19 |
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49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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20 <token name="@CHROMOSOME_LIST@"> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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21 #if $chromosome_list: |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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22 #set $chromosomes = [] |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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23 #for $chrom in $chromosome_list: |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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24 #silent $chromosomes.append("'%s'" % $chrom.chromosomes) |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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25 #end for |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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26 #set $chromosome_string = ' '.join($chromosomes) |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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27 --chromosomes $chromosome_string |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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28 #end if |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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29 </token> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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30 |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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31 <xml name="chromosome_list"> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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32 <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included."> |
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03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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33 <param argument="--chromosomes" type="text" value=""> |
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49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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34 <validator type="empty_field" /> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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35 </param> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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36 </repeat> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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37 </xml> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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38 |
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a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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39 <xml name="citations"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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40 <citations> |
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977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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41 <citation type="doi">10.1093/nar/gkaa220</citation> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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42 <citation type="doi">10.1093/nar/gky504</citation> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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43 <yield /> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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44 </citations> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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45 </xml> |
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03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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46 <xml name="dpi"> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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47 <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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48 </xml> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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49 |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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50 <xml name="restrictionCutFile"> |
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f72063d9426b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03
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51 <param argument="--restrictionCutFile" type="data" format="bed" optional="false" label="BED file with all restriction cut places" help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments |
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03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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52 (i.e. the region between one restriction site and the next)." /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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53 </xml> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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54 |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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55 <xml name="restrictionSequence"> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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56 <param argument="--restrictionSequence" type="text" optional="false" label="Sequence of the restriction site" help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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57 "dangling-ends". If not given, such statistics will not be available."> |
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f72063d9426b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03
iuc
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58 <validator type="regex" message="Only space separated nucleotide sequences are allowed.">^(?:[ATCGatcg]+(?:\s[ATCGatcg]+)*)?$</validator> |
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03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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59 </param> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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60 </xml> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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61 <xml name="danglingSequence"> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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62 <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting. |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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63 Each restriction enzyme recognizes a different DNA sequence and, |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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64 after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence. |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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65 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT. |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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66 For DpnII, the restriction site and dangling end sequence are the same: GATC. |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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67 This information is easily found on the description of the restriction enzyme. |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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68 The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads. |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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69 A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "> |
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f72063d9426b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03
iuc
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70 <validator type="regex" message="Only space separated nucleotide sequences are allowed.">^(?:[ATCGatcg]+(?:\s[ATCGatcg]+)*)?$</validator> |
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03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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71 </param> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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72 </xml> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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73 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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74 <xml name="zMax"> |
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03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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75 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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76 <!-- this should only be enabled when both or 3d is selected for param whatToShow --> |
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77 </xml> |
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78 <xml name="use_range"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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79 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range --> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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80 <param name="select_use_range" argument="--range" type="select" label="Range restriction (in bp)" help="If given, only counts within the specified range are considered."> |
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81 <option value="no_use_range">No restriction</option> |
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82 <option value="yes_use_range">Only consider counts within a range</option> |
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83 </param> |
17
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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84 <when value="no_use_range" /> |
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85 <when value="yes_use_range"> |
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86 <expand macro='range' /> |
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87 </when> |
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88 </conditional> |
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89 </xml> |
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90 |
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91 <xml name="range"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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92 <param name='range_min' type="integer" value="" min="0" label="Minimum range to consider interactions" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions." /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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93 <param name='range_max' type="integer" value="" min="0" label="Maximum range to consider interactions" /> |
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94 </xml> |
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95 |
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96 <xml name="colormap"> |
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97 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> |
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98 <option value="RdYlBu">RdYlBu</option> |
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99 <option value="Accent">Accent</option> |
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100 <option value="Spectral">Spectral</option> |
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101 <option value="Set1">Set1</option> |
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102 <option value="Set2">Set2</option> |
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103 <option value="Set3">Set3</option> |
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104 <option value="Dark2">Dark2</option> |
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105 <option value="Reds">Reds</option> |
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106 <option value="Oranges">Oranges</option> |
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107 <option value="Greens">Greens</option> |
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108 <option value="Blues">Blues</option> |
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109 <option value="Greys">Greys</option> |
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110 <option value="Purples">Purples</option> |
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111 <option value="Paired">Paired</option> |
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112 <option value="Pastel1">Pastel1</option> |
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113 <option value="Pastel2">Pastel2</option> |
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114 <option value="spring">spring</option> |
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115 <option value="summer">summer</option> |
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116 <option value="autumn">autumn</option> |
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117 <option value="winter">winter</option> |
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118 <option value="hot">hot</option> |
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119 <option value="coolwarm">coolwarm</option> |
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120 <option value="cool">cool</option> |
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121 <option value="seismic">seismic</option> |
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122 <option value="terrain">terrain</option> |
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123 <option value="ocean">ocean</option> |
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124 <option value="rainbow">rainbow</option> |
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125 <option value="bone">bone</option> |
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126 <option value="flag">flag</option> |
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127 <option value="prism">prism</option> |
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128 <option value="cubehelix">cubehelix</option> |
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129 <option value="binary">binary</option> |
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130 <option value="pink">pink</option> |
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131 <option value="gray">gray</option> |
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132 <option value="copper">copper</option> |
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133 <option value="BrBG">BrBG</option> |
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134 <option value="BuGn">BuGn</option> |
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135 <option value="BuPu">BuPu</option> |
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136 <option value="GnBu">GnBu</option> |
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137 <option value="OrRd">OrRd</option> |
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138 <option value="PiYG">PiYG</option> |
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139 <option value="PRGn">PRGn</option> |
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140 <option value="PuOr">PuOr</option> |
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141 <option value="PuRd">PuRd</option> |
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142 <option value="PuBu">PuBu</option> |
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143 <option value="RdBu">RdBu</option> |
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144 <option value="RdGy">RdGy</option> |
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145 <option value="RdPu">RdPu</option> |
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146 <option value="YlGn">YlGn</option> |
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147 <option value="PuBuGn">PuBuGn</option> |
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148 <option value="RdYlGn">RdYlGn</option> |
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149 <option value="YlGnBu">YlGnBu</option> |
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150 <option value="YlOrBr">YlOrBr</option> |
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151 <option value="YlOrRd">YlOrRd</option> |
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152 <option value="gist_gray">gist_gray</option> |
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153 <option value="gist_stern">gist_stern</option> |
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154 <option value="gist_earth">gist_earth</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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155 <option value="gist_yarg">gist_yarg</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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156 <option value="gist_ncar">gist_ncar</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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157 <option value="gist_rainbow">gist_rainbow</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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158 <option value="gist_heat">gist_heat</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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159 <option value="gnuplot">gnuplot</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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160 <option value="gnuplot2">gnuplot2</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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161 <option value="CMRmap">CMRmap</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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162 <option value="bwr">bwr</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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163 <option value="hsv">hsv</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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164 <option value="brg">brg</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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165 <option value="jet">jet</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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166 <option value="afmhot">afmhot</option> |
11
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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167 <option value="plasma">plasma</option> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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168 <option value="Accent_r">Accent reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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169 <option value="Spectral_r">Spectral reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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170 <option value="Set1_r">Set1 reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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171 <option value="Set2_r">Set2 reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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172 <option value="Set3_r">Set3 reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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173 <option value="Dark2_r">Dark2 reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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174 <option value="Reds_r">Reds reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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175 <option value="Oranges_r">Oranges reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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176 <option value="Greens_r">Greens reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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177 <option value="Blues_r">Blues reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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178 <option value="Greys_r">Greys reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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179 <option value="Purples_r">Purples reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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180 <option value="Paired_r">Paired reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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181 <option value="Pastel1_r">Pastel1 reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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182 <option value="Pastel2_r">Pastel2 reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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183 <option value="spring_r">spring reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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184 <option value="summer_r">summer reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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185 <option value="autumn_r">autumn reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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186 <option value="winter_r">winter reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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187 <option value="hot_r">hot reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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188 <option value="coolwarm_r">coolwarm reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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189 <option value="cool_r">cool reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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190 <option value="seismic_r">seismic reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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191 <option value="terrain_r">terrain reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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192 <option value="ocean_r">ocean reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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193 <option value="rainbow_r">rainbow reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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194 <option value="bone_r">bone reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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195 <option value="flag_r">flag reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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196 <option value="prism_r">prism reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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197 <option value="cubehelix_r">cubehelix reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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198 <option value="binary_r">binary reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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199 <option value="pink_r">pink reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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200 <option value="gray_r">gray reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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201 <option value="copper_r">copper reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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202 <option value="BrBG_r">BrBG reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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203 <option value="BuGn_r">BuGn reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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204 <option value="BuPu_r">BuPu reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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205 <option value="GnBu_r">GnBu reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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206 <option value="OrRd_r">OrRd reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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207 <option value="PiYG_r">PiYG reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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208 <option value="PRGn_r">PRGn reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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209 <option value="PuOr_r">PuOr reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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210 <option value="PuRd_r">PuRd reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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211 <option value="PuBu_r">PuBu reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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212 <option value="RdBu_r">RdBu reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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213 <option value="RdGy_r">RdGy reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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214 <option value="RdPu_r">RdPu reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
215 <option value="YlGn_r">YlGn reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
216 <option value="PuBuGn_r">PuBuGn reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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217 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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218 <option value="RdYlGn_r">RdYlGn reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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219 <option value="YlGnBu_r">YlGnBu reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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220 <option value="YlOrBr_r">YlOrBr reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
221 <option value="YlOrRd_r">YlOrRd reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
222 <option value="gist_gray_r">gist_gray reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
223 <option value="gist_stern_r">gist_stern reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
224 <option value="gist_earth_r">gist_earth reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
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changeset
|
225 <option value="gist_yarg_r">gist_yarg reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
226 <option value="gist_ncar_r">gist_ncar reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
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|
227 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
228 <option value="gist_heat_r">gist_heat reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
229 <option value="gnuplot_r">gnuplot reversed</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
230 <option value="gnuplot2_r">gnuplot2 reversed</option> |
a1cf508bff84
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231 <option value="CMRmap_r">CMRmap reversed</option> |
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232 <option value="bwr_r">bwr reversed</option> |
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233 <option value="hsv_r">hsv reversed</option> |
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234 <option value="brg_r">brg reversed</option> |
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235 <option value="jet_r">jet reversed</option> |
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236 <option value="afmhot_r">afmhot reversed</option> |
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237 <option value="plasma_r">plasma reversed</option> |
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238 </param> |
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239 </xml> |
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240 |
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241 <xml name="multiple_input_matrices"> |
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242 <repeat name="input_files" title="Hi-C Matrix files" min="2"> |
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243 <param name="matrix" type="data" format="h5,cool" label="Hi-C Matrix file" help="" /> |
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244 <param name="mlabel" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead." /> |
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245 </repeat> |
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246 </xml> |
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247 |
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248 <token name="@multiple_input_matrices@"> |
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249 #set $matrices = [] |
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250 #set $mlabels = [] |
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251 #for $counter, $i in enumerate($input_files): |
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252 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext'; |
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253 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext)) |
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254 |
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255 #if str($i.mlabel.value) != "": |
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256 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)] |
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257 #else |
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258 #set $mlabels += ['\'%s\'' % ($i.matrix.name)] |
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259 #end if |
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260 #end for |
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261 #set $mlabels = ' '.join($mlabels) |
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262 #set $matrices = ' '.join($matrices) |
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263 </token> |
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264 |
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265 <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token> |
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266 <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token> |
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267 <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token> |
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268 |
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269 <xml name="region"> |
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270 <param argument="--region" type="text" label="Region of the genome to limit the operation" help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500"> |
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271 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">not value or value.replace(':', '').replace('-', '').isalnum()</validator> |
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272 </param> |
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273 </xml> |
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274 |
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275 <xml name="kmeans_clustering"> |
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276 <conditional name="used_multiple_regions"> |
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277 <param name="used_multiple_regions_options" type="select" label="Did you compute the matrix with more than one groups of regions?" help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions."> |
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278 <option value="yes">Yes, I used multiple groups of regions</option> |
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279 <option value="no">No, I used only one group</option> |
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280 </param> |
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281 <when value="no"> |
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282 <conditional name="clustering"> |
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283 <param name="clustering_options" type="select" label="Clustering algorithm"> |
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284 <option value="none">No clustering</option> |
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285 <option value="kmeans">Kmeans clustering</option> |
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286 </param> |
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287 <when value="kmeans"> |
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288 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)." /> |
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289 </when> |
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290 <when value="none" /> |
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291 </conditional> |
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292 </when> |
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293 <when value="yes" /> |
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294 </conditional> |
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295 </xml> |
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296 |
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297 <token name="@KMEANS_CLUSTERING@"> |
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298 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
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299 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
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300 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
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301 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
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302 #end if |
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303 #end if |
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304 #end if |
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305 </token> |
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306 |
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307 <xml name="samFlag"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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308 <param name="samFlag" type="integer" optional="true" value="" label="Filter reads based on the SAM flag" help="For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)" /> |
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309 </xml> |
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310 <xml name="plotNumbers"> |
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311 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" label="Plot the correlation value" help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)" /> |
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312 </xml> |
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313 <xml name="doNotExtendPairedEnds"> |
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314 <param argument="--doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" label="Do not extend paired ends" help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)" /> |
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315 </xml> |
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316 <xml name="ignoreDuplicates"> |
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317 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" label="Ignore duplicates" help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" /> |
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318 </xml> |
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319 <xml name="minMappingQuality"> |
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320 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1" label="Minimum mapping quality" help= "If set, only reads that have a mapping quality score higher than the given value are considered. |
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321 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. |
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322 A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere." /> |
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323 </xml> |
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324 |
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325 <xml name="skipZeros"> |
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326 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" label="Skip zeros" help="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" /> |
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327 </xml> |
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328 |
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329 <xml name="fragmentLength"> |
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330 <param argument="--fragmentLength" type="integer" value="300" min="1" label="Fragment length used for the sequencing" help="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)" /> |
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331 </xml> |
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332 |
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333 <xml name="scaleFactor"> |
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334 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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335 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)" /> |
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336 </xml> |
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337 <xml name="xMax"> |
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338 <param argument="--xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" /> |
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339 </xml> |
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340 <xml name="filterThreshold"> |
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341 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect." /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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342 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0" label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect." /> |
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343 </xml> |
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344 <xml name="pseudocount"> |
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345 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero." /> |
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346 </xml> |
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347 <xml name='matrix_h5_cooler_macro'> |
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348 <param name='matrix_h5_cooler' type="data" format="h5,cool" label="Matrix to compute on" /> |
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349 </xml> |
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350 <xml name='matrix_h5_cooler_multiple_macro'> |
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351 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" /> |
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352 </xml> |
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353 |
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354 <xml name='matrix_cooler_multiple_macro'> |
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355 <param name='matrix_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Hi-C matrix" /> |
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356 </xml> |
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357 <xml name='convertFormat_single_macro'> |
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358 <conditional name="inputFormat_conditional"> |
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359 <param name="inputFormat_selector" type="select" label="Choose input file type"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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360 <option value="optionCool" selected="True">cool</option> |
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361 <option value="optionH5">h5</option> |
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362 <option value="optionHic">hic</option> |
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363 <option value="optionHomer">Homer</option> |
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364 <option value="optionHicpro">HiCPro</option> |
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365 <option value="option2Dtext">2D-text</option> |
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366 |
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367 </param> |
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368 <when value="optionCool"> |
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369 <expand macro='matrix_h5_cooler_macro' /> |
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370 <param name='correctionName' type='text' label='Correction factors column name' /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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371 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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372 <param name='chromosome' type='text' label='Load only one chromosome' /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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373 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' /> |
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374 </when> |
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375 <when value="optionH5"> |
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376 <expand macro='matrix_h5_cooler_macro' /> |
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377 </when> |
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378 <when value="optionHic"> |
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379 <param name='matrixHic' type='data' format='hic' label='.hic matrix' /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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380 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'"> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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|
381 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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382 </param> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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383 </when> |
11
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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384 <when value="optionHomer"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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385 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' /> |
11
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
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386 </when> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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387 <when value="optionHicpro"> |
19
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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388 <param name='matrixHicpro' type='data' format='txt' label='.hicpro matrix' /> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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389 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' /> |
11
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
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390 </when> |
19
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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391 <when value="option2Dtext"> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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392 <param name='matrix2Dtext' type='data' format='txt' label='A 2D text matrix' /> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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393 |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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394 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'"> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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395 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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396 </param> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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397 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' /> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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398 </when> |
11
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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399 </conditional> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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400 </xml> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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401 |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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402 <xml name='convertFormat_multiple_macro'> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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403 <conditional name="inputFormat_conditional"> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
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404 <param name="inputFormat_selector" type="select" label="Choose input file type"> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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405 <option value="optionCool" selected="True">cool</option> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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406 <option value="optionH5">h5</option> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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407 <option value="optionHomer">Homer</option> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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408 <option value="optionHicpro">HiCPro</option> |
19
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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409 <option value="option2Dtext">2D-text</option> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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410 |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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411 |
11
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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412 </param> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
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413 <when value="optionCool"> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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414 <expand macro='matrix_h5_cooler_multiple_macro' /> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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415 <param name='correctionName' type='text' label='Correction factors column name' /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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416 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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417 <param name='chromosome' type='text' label='Load only one chromosome' /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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418 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' /> |
11
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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419 </when> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
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420 <when value="optionH5"> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
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421 <expand macro='matrix_h5_cooler_multiple_macro' /> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
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422 </when> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
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423 <when value="optionHomer"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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424 <param name='matrixHomer' type='data' format='txt' multiple="true" label='Homer interaction matrix' /> |
11
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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425 </when> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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426 <when value="optionHicpro"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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427 <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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428 <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' /> |
11
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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429 </when> |
19
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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430 <when value="option2Dtext"> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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431 <param name='matrix2Dtext' type='data' format='txt' multiple="true" label='A 2D text matrix' /> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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432 |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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433 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'"> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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434 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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435 </param> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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436 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' /> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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437 </when> |
11
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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438 </conditional> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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439 </xml> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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440 <xml name='convertFormat_single_output_macro'> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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441 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> --> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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442 <conditional name="outputFormat_conditional"> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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443 <param name="outputFormat_selector" type="select" label="Choose output file type"> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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444 <option value="cool" selected="True">cool</option> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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445 <option value="h5">h5</option> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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446 <option value="homer">Homer</option> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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447 <option value="ginteractions">ginteractions</option> |
19
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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448 <option value="hicpro">hicpro</option> |
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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449 |
11
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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450 </param> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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451 <when value="cool"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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452 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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453 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' /> |
11
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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|
454 </when> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
16
diff
changeset
|
455 <when value='h5' /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
16
diff
changeset
|
456 <when value='homer' /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
16
diff
changeset
|
457 <when value='ginteractions' /> |
19
977dc15add20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
18
diff
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|
458 <when value='hicpro' /> |
11
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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459 </conditional> |
49c8055f6830
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff
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|
460 </xml> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
461 <token name="@REFERENCES@"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
462 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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463 .. class:: infomark |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
464 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
465 For more information on the tools, please visit our `help site`_. |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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466 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
467 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
468 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
469 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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470 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
471 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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472 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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473 .. _help site: https://hicexplorer.readthedocs.org |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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474 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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475 </token> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
476 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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477 <xml name="multiple_input_bams"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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478 <repeat name="input_files" title="BAM files" min="2"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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479 <param name="bamfile" type="data" format="bam" label="BAM file" /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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480 <param name="label" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead." /> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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481 </repeat> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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482 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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483 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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484 <xml name="multiple_input_bigwigs"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
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|
485 <repeat name="input_files" title="BigWig files" min="2"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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486 <param name="bigwigfile" type="data" format="bigwig" label="Bigwig file" /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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487 <param name="label" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead."> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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488 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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489 </param> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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490 </repeat> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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491 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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492 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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493 <xml name="plotTitle"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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494 <param name="plotTitle" type="text" value="" optional="True" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. (--plotTitle)"> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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495 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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496 </param> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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497 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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498 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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499 <token name="@multiple_input_bams@"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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500 #import tempfile |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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501 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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502 #set files=[] |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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503 #set labels=[] |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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504 #for $i in $input_files: |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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505 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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506 #set $temp_input_path = $temp_input_handle.name |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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507 #silent $temp_input_handle.close() |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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508 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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509 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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510 #silent $files.append('%s.bam' % $temp_input_path) |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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511 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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512 ##set $files += [str($i.bamfile)] |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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513 #if str($i.label.value) != "": |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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514 #set $labels += ["\"%s\"" % ($i.label.value)] |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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515 #else |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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516 #set $labels += ["\"%s\"" % ($i.bamfile.name)] |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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517 #end if |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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518 #end for |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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519 </token> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
520 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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521 <token name="@multiple_input_bigwigs@"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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522 #import tempfile |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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523 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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524 #set files=[] |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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525 #set labels=[] |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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526 #for $i in $input_files: |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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527 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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528 #set $temp_input_path = $temp_input_handle.name |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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529 #silent $temp_input_handle.close() |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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530 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path)) |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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531 #silent $files.append('%s.bw' % $temp_input_path) |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
532 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
533 ##set $files += [str($i.bigwigfile)] |
a1cf508bff84
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534 #if str($i.label.value) != "": |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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535 #set $labels += ["\"%s\"" % ($i.label.value)] |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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536 #else |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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537 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)] |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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538 #end if |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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539 #end for |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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540 </token> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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541 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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542 <xml name="reference_genome_source"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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543 <conditional name="source"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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544 <param name="ref_source" type="select" label="Reference genome"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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545 <option value="cached">locally cached</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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546 <option value="history">in your history</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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547 </param> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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548 <when value="cached"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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549 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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550 <options from_data_table="deepTools_seqs"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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551 <filter type="sort_by" column="1" /> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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552 <validator type="no_options" message="No indexes are available." /> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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553 </options> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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554 </param> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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555 </when> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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556 <when value="history"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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557 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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558 </when> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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559 </conditional> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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560 </xml> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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561 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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562 <token name="@reference_genome_source@"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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563 #if $source.ref_source=="history": |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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564 --genome $source.input1 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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565 #else: |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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566 --genome "${source.input1_2bit.fields.path}" |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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567 #end if |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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568 </token> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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569 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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570 <xml name="effectiveGenomeSize"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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571 <conditional name="effectiveGenomeSize"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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572 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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573 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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574 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes."> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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575 <option value="93260000">ce10 (93260000)</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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576 <option value="121400000">dm3 (121400000)</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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577 <option value="2451960000" selected="true">hg19 (2451960000)</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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578 <option value="2150570000">mm9 (2150570000)</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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579 <option value="specific">user specified</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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580 </param> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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581 <when value="specific"> |
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03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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582 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000" /> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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583 </when> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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584 <when value="2150570000" /> |
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585 <when value="2451960000" /> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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586 <when value="121400000" /> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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587 <when value="93260000" /> |
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588 </conditional> |
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589 </xml> |
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590 |
a1cf508bff84
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591 <xml name="image_file_format"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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592 <param name="outFileFormat" type="select" label="Image file format"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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593 <option value="png" selected="true">png</option> |
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594 <option value="pdf">pdf</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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595 <option value="svg">svg</option> |
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596 <option value="eps">eps</option> |
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597 <option value="emf">emf</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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598 </param> |
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599 </xml> |
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600 |
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601 <xml name="missingDataAsZero"> |
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03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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602 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Treat missing data as zero" help="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." /> |
0
a1cf508bff84
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603 </xml> |
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604 |
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605 <xml name="input_save_matrix_values"> |
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03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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606 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" /> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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607 </xml> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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608 |
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609 <xml name="input_graphic_output_settings"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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610 <conditional name="output"> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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611 <param name="showOutputSettings" type="select" label="Show advanced output settings"> |
0
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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612 <option value="no" selected="true">no</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
613 <option value="yes">yes</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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changeset
|
614 </param> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
changeset
|
615 <when value="no" /> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff
changeset
|
616 <when value="yes"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
617 <yield /> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
16
diff
changeset
|
618 <param name="saveData" type="boolean" label="Save the data underlying the average profile" /> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
16
diff
changeset
|
619 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap." /> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
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changeset
|
620 </when> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
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diff
changeset
|
621 </conditional> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
622 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
623 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
624 <xml name="input_image_file_format"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
625 <param name="outFileFormat" type="select" label="Image file format"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
626 <option value="png" selected="true">png</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
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diff
changeset
|
627 <option value="pdf">pdf</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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changeset
|
628 <option value="svg">svg</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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changeset
|
629 <option value="eps">eps</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff
changeset
|
630 <option value="emf">emf</option> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
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changeset
|
631 </param> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
632 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
633 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
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|
634 <xml name="output_image_file_format"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
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changeset
|
635 <data format="png" name="outFileName" label="${tool.name} image"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
changeset
|
636 <change_format> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
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changeset
|
637 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
638 <when input="output.outFileFormat" value="svg" format="svg" /> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
639 <when input="output.outFileFormat" value="eps" format="eps" /> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
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|
640 <when input="output.outFileFormat" value="emf" format="emf" /> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
641 </change_format> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
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changeset
|
642 </data> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
643 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
644 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
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|
645 <xml name="output_save_matrix_values"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
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|
646 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
647 <filter> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
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|
648 (( |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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649 output['showOutputSettings'] == 'yes' and |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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650 output['saveMatrix'] is True |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
changeset
|
651 )) |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
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|
652 </filter> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
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changeset
|
653 </data> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
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|
654 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
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|
655 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
656 <xml name="output_graphic_outputs"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
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|
657 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
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|
658 <filter> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
659 (( |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
660 output['showOutputSettings'] == 'yes' and |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
changeset
|
661 output['saveData'] is True |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
changeset
|
662 )) |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
663 </filter> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
changeset
|
664 </data> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
665 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
changeset
|
666 <filter> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
667 (( |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
668 output['showOutputSettings'] == 'yes' and |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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changeset
|
669 output['saveSortedRegions'] is True |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
670 )) |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
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|
671 </filter> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
changeset
|
672 </data> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
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|
673 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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|
674 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
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|
675 <xml name="track_input_h5_macro"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
16
diff
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|
676 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format" /> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
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|
677 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
678 <xml name="track_input_bed_macro"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
16
diff
changeset
|
679 <param name="track_input_bed" type="data" format="bed" label="Track file BED format" /> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
changeset
|
680 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
681 <xml name="track_input_bedgraph_macro"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
16
diff
changeset
|
682 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" /> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
683 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
684 <xml name="track_input_bigwig_macro"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
16
diff
changeset
|
685 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" /> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
changeset
|
686 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
687 <xml name="track_input_bedgraph_matrix_macro"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
16
diff
changeset
|
688 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" /> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents:
diff
changeset
|
689 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
diff
changeset
|
690 <xml name="track_input_tabular_macro"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
16
diff
changeset
|
691 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format" /> |
0
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
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changeset
|
692 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents:
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changeset
|
693 <xml name="plot_title"> |
17
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
16
diff
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694 <param name="title" type="text" optional="true" label="Plot title"> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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695 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator> |
03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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696 </param> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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697 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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698 |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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699 <xml name="spacer_macro"> |
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03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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700 <param name="spacer_width" type="float" value="" min="0" optional="True" label="Include spacer at the end of the track" help="Width of the spacer." /> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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701 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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702 <xml name="fontsize_macro"> |
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03dd3c16ae4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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703 <param name="fontsize" type="integer" value="" min="5" optional="True" label="Fontsize" /> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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704 </xml> |
a1cf508bff84
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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705 </macros> |